Retrotransposons-based genetic regulation underlies the cellular response to two genetically diverse viral infections in tomato

Physiological and Molecular Plant Pathology - Tập 120 - Trang 101839 - 2022
Ajeet Singh1, Suneha Goswami1, T. Vinutha1, R.K. Jain2, S.V. Ramesh3, Shelly Praveen1
1Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
2Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
3Division of Physiology, Biochemistry and Post-Harvest Technology, ICAR-Central Plantation Crops Research Institute, Kasaragod, Kerala, 671124, India

Tài liệu tham khảo

Estep, 2013, The dynamics of LTR retrotransposon accumulation across 25 million years of panicoid grass evolution, Heredity, 110, 194, 10.1038/hdy.2012.99 Bennetzen, 1996, The contributions of retroelements to plant genome organization, function and evolution, Trends Microbiol., 4, 347, 10.1016/0966-842X(96)10042-1 Kumar, 1996, The adventures of the Ty1-copia group of retrotransposons in plants, Trends Genet., 12, 41, 10.1016/0168-9525(96)81393-X SanMiguel, 1996, Nested retrotransposons in the intergenic regions of the maize genome, Science, 274, 765, 10.1126/science.274.5288.765 Grandbastien, 2005, Stress activation and genomic impact of Tnt1 retrotransposons in Solanaceae, Cytogenet. Genome Res., 110, 229, 10.1159/000084957 Ramakrishnan, 2021, The dynamism of transposon methylation for plant development and stress adaptation, Int. J. Mol. Sci., 22, 10.3390/ijms222111387 Kumar, 1999, Plant retrotransposons, Annu. Rev. Genet., 33, 479, 10.1146/annurev.genet.33.1.479 Kashkush, 2013, Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat, Nat. Genet., 33, 102, 10.1038/ng1063 Kashkush, 2007, Large-scale survey of cytosine methylation of retrotransposons and the impact of readout transcription from long terminal repeats on expression of adjacent rice genes, Genetics, 177, 1975, 10.1534/genetics.107.080234 McClintock, 1984, The significance of responses of the genome to challenge, Science, 226, 792, 10.1126/science.15739260 Grandbastien, 1998, Activation of plant retrotransposons under stress conditions, Trends Plant Sci., 3, 181, 10.1016/S1360-1385(98)01232-1 Arias, 2012, Infectious agents associated with schizophrenia: a meta-analysis, Schizophr. Res., 136, 128, 10.1016/j.schres.2011.10.026 Bui, 2012, LTR retrotransposons as controlling elements of genome response to stress?, 273 Anca, 2014, Different tobacco retrotransposons are specifically modulated by the elicitor cryptogein and reactive oxygen species, J. Plant Physiol., 171, 1533, 10.1016/j.jplph.2014.07.003 Goodier, 2016, Restricting retrotransposons: a review, Mobile DNA, 7, 16, 10.1186/s13100-016-0070-z Hirochika, 2013, Activation of tobacco retrotransposons during tissue culture, EMBO J., 12, 2521, 10.1002/j.1460-2075.1993.tb05907.x Konieczny, 1991, A superfamily of Arabidopsis thaliana retrotransposons, Genetics, 127, 801, 10.1093/genetics/127.4.801 Sasaki, 2002, The genome sequence and structure of rice chromosome 1, Nature, 420, 312, 10.1038/nature01184 Hirochika, 1996, Retrotransposons of rice involved in mutations induced by tissue culture, Proc. Natl. Acad. Sci. U.S.A., 93, 7783, 10.1073/pnas.93.15.7783 Pouteau, 1991, Specific expression of the tobacco Tnt1 retrotransposon in protoplasts, EMBO J., 10, 1911, 10.1002/j.1460-2075.1991.tb07717.x Hirochika, 1995, Extrachromosomal circular forms of the tobacco retrotransposon-Tto1, Gene, 165, 229, 10.1016/0378-1119(95)00581-P Moreau-Mhiri, 1996, Regulation of expression of the tobacco Tnt1 retrotransposon in heterologous species following pathogen-related stresses, Plant J., 9, 409, 10.1046/j.1365-313X.1996.09030409.x Grandbastien, 1997, The expression of the tobacco Tnt1 retrotransposon is linked to plant defense responses, Genetica, 100, 241, 10.1023/A:1018302216927 Mhiri, 1997, The promoter of the tobacco Tnt1 retrotransposon is induced by wounding and by abiotic stress, Plant Mol. Biol., 33, 257, 10.1023/A:1005727132202 Takeda, 2001, Linear DNA intermediates of the Tto1 retrotransposon in Gag particles accumulated in stressed tobacco and Arabidopsis thaliana, Plant J., 28, 307, 10.1046/j.1365-313X.2001.01151.x Scandalios, 1993, Oxygen stress and superoxide dismutases, Plant Physiol., 101, 7, 10.1104/pp.101.1.7 Apel, 2004, Reactive oxygen species: metabolism, oxidative stress, and signal transduction, Annu. Rev. Plant Biol., 55, 373, 10.1146/annurev.arplant.55.031903.141701 Sagi, 2006, Production of reactive oxygen species by plant NADPH oxidases, Plant Physiol., 141, 336, 10.1104/pp.106.078089 Torres, 2006, Reactive oxygen species signaling in response to pathogens, Plant Physiol., 141, 373, 10.1104/pp.106.079467 Mittler, 2017, ROS are good, Trends Plant Sci., 22, 11, 10.1016/j.tplants.2016.08.002 Waszczak, 2018, Reactive oxygen species in plant signaling, Annu. Rev. Plant Biol., 69, 209, 10.1146/annurev-arplant-042817-040322 Caverzan, 2016, Reactive oxygen species and antioxidant enzymes involved in plant tolerance to stress Permar, 2014, Tospo viral infection instigates necrosis and premature senescence by micro RNA controlled programmed cell death in Vigna unguiculata, Physiol. Mol. Plant Pathol., 88, 77, 10.1016/j.pmpp.2014.09.004 Niu, 2016, Hydrogen peroxide signaling in plant development and abiotic responses: crosstalk with nitric oxide and calcium, Front. Plant Sci., 7, 230, 10.3389/fpls.2016.00230 Van, 2006, Reactive oxygen species in plant cell death, Plant Physiol., 141, 384, 10.1104/pp.106.078295 Desikan, 1998, Harpin and hydrogen peroxide both initiate programmed cell death but have differential effects on defence gene expression in Arabidopsis suspension cultures, Biochem. J., 330, 115, 10.1042/bj3300115 Singh, 2018, Effect of temperature on symptoms expression and viral RNA accumulation in Groundnut bud necrosis virus infected Vigna unguiculata, Iran. J. Biotechnol., 16, 10.21859/ijb.1846 Culver, 2007, Virus-induced disease: altering host physiology one interaction at a time, Annu. Rev. Phytopathol., 45, 221, 10.1146/annurev.phyto.45.062806.094422 German, 1992, Tospoviruses: diagnosis, molecular biology, phylogeny, and vector relationships, Annu. Rev. Phytopathol., 30, 315, 10.1146/annurev.py.30.090192.001531 Kumar, 2017, Possible role of miRNAs and their targets, in modulating leaf morphology and plant growth during leaf curl virus infection in tomato, Indian J. Plant Physiol., 22, 608, 10.1007/s40502-017-0345-5 Jyothsna, 2013, Infection of Tomato Leaf Curl New Delhi Virus (ToLCNDV), a bipartite begomovirus with betasatellites, results in enhanced level of helper virus components and antagonistic interaction between DNA B and betasatellites, Appl. Microbiol. Biotechnol., 97, 5457, 10.1007/s00253-012-4685-9 Kaur, 2015, Gene expression changes in tomato during symptom development in response to leaf curl virus infection, J. Plant Biochem. Biotechnol., 24, 347, 10.1007/s13562-014-0280-8 Koundal, 2010, Modulation of plant development and MYB down regulation: both during in planta expression of miR159a and in natural ToLCV infection, J. Plant Biochem. Biotechnol., 19, 10.1007/BF03263337 Sahana, 2012, Inhibition of the host proteasome facilitates Papaya ringspot virus accumulation and proteosomal catalytic activity is modulated by viral factor HcPro, PLoS One, 7, 10.1371/journal.pone.0052546 Tamari, 2013, A comparison of DNA extraction methods using petunia hybrida tissues, J. Biomol. Tech., 24, 113 Ramesh, 2019, Quantification of a legume begomovirus to evaluate soybean genotypes for yellow mosaic disease (YMD) resistance, J. Virol Methods, 268, 24, 10.1016/j.jviromet.2019.03.002 Frew, 1983, Spectrophotometric determination of hydrogen peroxide and organic hydroperoxides at low concentrations in aqueous solution, Anal. Chim. Acta, 155, 139, 10.1016/S0003-2670(00)85587-7 Turner, 1974, The quantitative relation between plant and bacterial cells involved in the hypersensitive reaction, Phytopathology, 64, 885, 10.1094/Phyto-64-885 Hirayama, 2010, Research on plant abiotic stress responses in the post-genome era: past, present and future, Plant J., 61, 1041, 10.1111/j.1365-313X.2010.04124.x Avramova, 2015, Transcriptional ‘memory’ of a stress: transient chromatin and memory (epigenetic) marks at stress-response genes, Plant J., 83, 149, 10.1111/tpj.12832 Johns, 1985, A low copy number, copia-like transposon in maize, EMBO J., 4, 1093, 10.1002/j.1460-2075.1985.tb03745.x Salazar, 2007, The promoter of the TLC1.1 retrotransposon from Solanum chilense is activated by multiple stress-related signaling molecules, Plant Cell Rep., 26, 1861, 10.1007/s00299-007-0375-y Grandbastien, 1989, Tnt1, a mobile retroviral-like transposable element of tobacco isolated by plant cell genetics, Nature, 337, 376, 10.1038/337376a0 Pouteau, 1994, Microbial elicitors of plant defence responses activate transposition of a retrotransposon, Plant J., 5, 535, 10.1046/j.1365-313X.1994.5040535.x Ricci, 1997, Induction of the hypersensitive response and systemic acquired resistance by fungal proteins: the case of elicitins Lherminier, 2009, NADPH oxidase-mediated reactive oxygen species production: subcellular localization and reassessment of its role in plant defense, Mol. Plant Microbe Interact., 22, 868, 10.1094/MPMI-22-7-0868 Hyodo, 2017, Roles of superoxide anion and hydrogen peroxide during replication of two unrelated plant RNA viruses in Nicotiana benthamiana, Plant Signal. Behav., 12, 10.1080/15592324.2017.1338223 Huang, 2009, Down-regulation of a SILENT INFORMATION REGULATOR2-related histone deacetylase gene, OsSRT1, induces DNA fragmentation and cell death in rice, Plant Physiol., 144, 1508, 10.1104/pp.107.099473 Perez, 2014, The role of ROS signaling in cross-tolerance: from model to crop, Front. Plant Sci., 5, 754, 10.3389/fpls.2014.00754 Liu, 2013, Transcriptional regulation of yeast oxidative phosphorylation hypoxic genes by oxidative stress, Antioxidants Redox Signal., 19, 10.1089/ars.2012.4589 Guilfoyle, 1998, How does auxin turn on genes?, Plant Physiol., 118, 341, 10.1104/pp.118.2.341 Li, 2020, Pepper crop improvement against cucumber mosaic virus (cmv): a review, Front. Plant Sci., 11, 10.3389/fpls.2020.598798 Machida, 2015, The complex of ASYMMETRIC LEAVES (AS) proteins plays a central role in antagonistic interactions of genes for leaf polarity specification in Arabidopsis, Wiley Interdiscip. Rev. Dev. Biol., 4, 655, 10.1002/wdev.196 Kohli, 2014, Identification and characterization of Wilt and salt stress-responsive MicroRNAs in chickpea through high-throughput sequencing, PLoS One, 9, 10.1371/journal.pone.0108851 Kim, 2007, A membrane associated NAC transcription factor regulates salt-responsive flowering via FLOWERING LOCUS T in Arabidopsis, Planta, 226, 647, 10.1007/s00425-007-0513-3 Guo, 2005, Micro RNA directs mRNA cleavage of the transcription factor NAC1 to down-regulate auxin signals for Arabidopsis lateral root development, Plant Cell, 17, 1376, 10.1105/tpc.105.030841 Vinutha, 2020, Tomato auxin biosynthesis/signaling is reprogrammed by the geminivirus to enhance its pathogenicity, Planta, 252, 51, 10.1007/s00425-020-03452-9 Muller, 2021, Assessing the impact of a viral infection on the expression of transposable elements in the cabbage looper moth (Trichoplusia ni), Genome Biol. Evol., 13, 10.1093/gbe/evab231 Deneweth, 2022, Nearby transposable elements impact plant stress gene regulatory networks: a meta-analysis in A. thaliana and S. lycopersicum, BMC Genom., 23, 18, 10.1186/s12864-021-08215-8